Bacterial Genomics and Bioinformatics Lab

URL: http://staff.vbi.vt.edu/jcslab/

Contact:

The lab develops various kinds of bioinformatics tools to help with genome  annotation and analyses. These include infrastructure (database and  interface) for community genome annotation and tools for comparative  genomics. We have worked primarily with genomes of bacterial pathogens.
 
2011
Dias, Z., U. Dias, and J. C. Setubal, "Using inversion signatures to generate draft genome scaffolds", ACM International Conference on Bioinformatics and Computational Biology 2011, Chicago, IL, 08/2011.
Potnis, N., K. Krasileva, V. Chow, N. F. Almeida, P. B. Patil, R. P. Ryan, M. Sharlach, F. Behlau, M. J. Dow, M. T. Momol, et al., "Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper", BMC Genomics, vol. 12, issue 1, pp. 146, 2011.
Wibberg, D., J. Blom, S. Jaenicke, F. Kollin, O. Rupp, B. Scharf, S. Schneiker-Bekel, R. Sczcepanowski, A. Goesmann, J. C. Setubal, et al., "Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid", Journal of Biotechnology, 2/2011.
Shulaev, V., D. J. Sargent, R. N. Crowhurst, T. C. Mockler, O. Folkerts, A. L. Delcher, P. Jaiswal, K. Mockaitis, A. Liston, S. P. Mane, et al., "The genome of woodland strawberry (Fragaria vesca)", Nature Genetics, vol. 43, issue 2, pp. 109 - 116, 2/2011.
Collen, P. N., J. Collen, M. S. Reis, M. Pedersen, J. C. Setubal, A. M. Varani, P. Colepicolo, and M. C. Oliveira, "Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta)", Journal of Applied Phycology, 05/2011. Abstract
Saldanha, H. V., E. Ribeiro, M. Holanda, A. Araujo, G. Rodrigues, M. E. Walter, J. C. Setubal, and A. Davila, "A cloud architecture for bioinformatics workflows", First International Conference on Cloud Computing and Services Science, 05/2011.
2010
Almeida, N. F., S. Yan, R. Cai, C. R. Clarke, C. E. Morris, N. W. Schaad, E. L. Schuenzel, G. H. Lacy, X. Sun, J. B. Jones, et al., "PAMDB, A Multilocus Sequence Typing and Analysis Database and Website for Plant-Associated Microbes", Phytopathology, vol. 100, issue 3, pp. 208 - 215, 03/2010.
Torto-Alalibo, T., C. W. Collmer, M. Gwinn-Giglio, M. Lindeberg, S. Meng, M. C. Chibucos, T. - T. Tseng, J. Lomax, B. Biehl, A. Ireland, et al., "Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology", Microbiology and Molecular Biology Reviews, vol. 74, issue 4, pp. 479 - 503, 12/2010.
Tiller, R. V., J. E. Gee, M. A. Frace, T. K. Taylor, J. C. Setubal, A. R. Hoffmaster, and B. K. De, "Characterization of Novel Brucella Strains Originating from Wild Native Rodent Species in North Queensland, Australia", Applied and Environmental Microbiology, vol. 76, issue 17, pp. 5837 - 5845, 09/2010.
Zhang, H., J. C. Setubal, X. Zhan, Z. Zheng, L. Yu, J. Wu, and D. Chen, "Component identification of electron transport chains in curdlan-producing Agrobacterium sp. ATCC 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis", Journal of Industrial Microbiology & Biotechnology, 2010.
Moreira, L. M., N. F. Almeida, N. Potnis, L. A. Digiampietri, S. S. Adi, J. C. Bortolossi, A. C. da Silva, A. M. da Silva, F. E. de Moraes, J. C. de Oliveira, et al., "Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii", BMC Genomics, vol. 11, issue 1, pp. 238, 2010.
Dias, U., Z. Dias, and J. C. Setubal, "A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes", RECOMB Comparative Genomics 2010, Ottawa, Canada, Springer, 10/2010.
Yang, K., and J. C. Setubal, "Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes", ACM International Conference on Bioinformatics and Computational Biology 2010, Niagara Falls, NY, ACM Digital Libraries, 08/2010.
Myers, E., P. S. Fisher, K. Irwin, J. Baek, and J. C. Setubal, "The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings", Pattern Recognition in Bioinformatics 2010, Nijmegen, The Netherlands, Springer, 10/2010.
2009
Dias-Neto, E., D. N. Nunes, R. J. Giordano, J. Sun, G. H. Botz, K. Yang, J. C. Setubal, R. Pasqualini, and W. Arap, "Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis", PLoS ONE, vol. 4, issue 12, pp. e8338, 12/2009.
Chibucos, M. C., T. - T. Tseng, and J. C. Setubal, "Describing commonalities in microbial effector delivery using the Gene Ontology", Trends in Microbiology, vol. 17, issue 7, pp. 312 - 319, 07/2009.
Setubal, J. C., P. dos Santos, B. S. Goldman, H. Ertesvag, G. Espin, L. M. Rubio, S. Valla, N. F. Almeida, D. Balasubramanian, L. Cromes, et al., "Genome Sequence of Azotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes", Journal of Bacteriology, vol. 191, issue 14, pp. 4534 - 4545, 07/2009.
Wattam, A. R., K. P. Williams, E. E. Snyder, N. F. Almeida, M. Shukla, A. W. Dickerman, O. R. Crasta, R. Kenyon, J. Lu, J. M. Shallom, et al., "Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle", Journal of Bacteriology, vol. 191, issue 11, pp. 3569 - 3579, 06/2009.
Tseng, T. - T., B. M. Tyler, and J. C. Setubal, "Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology", BMC Microbiology, vol. 9, issue Suppl 1, pp. S2, 2009.
Gillespie, J. J., N. C. Ammerman, S. M. Dreher-Lesnick, S. M. Rahman, M. J. Worley, J. C. Setubal, B. S. Sobral, and A. F. Azad, "An Anomalous Type IV Secretion System in Rickettsia Is Evolutionarily Conserved", PLoS ONE, vol. 4, issue 3, pp. e4833, 3/2009.
Slater, S. C., B. S. Goldman, B. Goodner, J. C. Setubal, S. K. Farrand, E. W. Nester, T. J. Burr, L. Banta, A. W. Dickerman, I. Paulsen, et al., "Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria", Journal of Bacteriology, vol. 191, issue 8, pp. 2501 - 2511, 04/2009.
Warren, A. S., and J. C. Setubal, "The Genome Reverse Compiler: an explorative annotation tool", BMC Bioinformatics, vol. 10, issue 1, pp. 35, 2009.
Almeida, N. F., S. Yan, M. Lindeberg, D. J. Studholme, D. J. Schneider, B. Condon, H. Liu, C. J. Viana, A. Warren, C. Evans, et al., "A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000", Molecular Plant-Microbe Interactions, vol. 22, issue 1, pp. 52 - 62, 01/2009.
2008
Watkinson, J. I., L. Hendricks, A. A. Sioson, L. S. Heath, H. J. Bohnert, and R. Grene, "Tuber Development Phenotypes in Adapted and Acclimated, Drought-stressed Solanum tuberosum ssp. andigena Have Distinct Expression Profiles of Genes Associated with Carbon Metabolism", Plant Physiology and Biochemistry, vol. 46, pp. pp. 34-45, 2008.
Gillespie, J. J., K. Williams, M. Shukla, E. E. Snyder, E. K. Nordberg, S. M. Ceraul, C. Dharmanolla, D. Rainey, J. Soneja, J. M. Shallom, et al., "Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life", PLoS ONE, vol. 3, issue 4, pp. e2018, 4/2008.
Yan, S., H. Liu, T. J. Mohr, J. Jenrette, R. Chiodini, M. Zaccardelli, J. C. Setubal, and B. A. Vinatzer, "Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain", Applied and Environmental Microbiology, vol. 74, issue 10, pp. 3171 - 3181, 05/2008.
2007
Venancio, T. M., R. DeMarco, G. T. Almeida, K. C. Oliveira, J. C. Setubal, and S. Verjovski-Almeida, "Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions", BMC Genomics, vol. 8, issue 1, pp. 407, 2007.
Yu, G. X., E. E. Snyder, S. M. Boyle, O. R. Crasta, M. Czar, S. P. Mane, A. Purkayastha, B. Sobral, and J. C. Setubal, "A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case", Nucleic Acids Research, vol. 35, issue 12, pp. 3953 - 3962, 06/2007.
Snyder, E. E., N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, et al., "PATRIC: The VBI PathoSystems Resource Integration Center", Nucleic Acids Research, vol. 35, issue Database, pp. D401 - D406, 01/2007.
2006
Setubal, J. C., M. Reis, J. Matsunaga, and D. A. Haake, "Lipoprotein computational prediction in spirochaetal genomes", Microbiology, vol. 152, issue 1, pp. 113 - 121, 01/2006.
LORENZINI, D., P. SILVAJR, M. SOARES, P. Arruda, J. C. Setubal, and S. DAFFRE, "Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana", Developmental & Comparative Immunology, vol. 30, issue 6, pp. 545 - 556, 2006.
2005
Setubal, J. C., L. MOREIRA, and A. DASILVA, "Bacterial phytopathogens and genome science", Current Opinion in Microbiology, vol. 8, issue 5, pp. 595 - 600, 10/2005.
Moreira, L. M., R. F. De Souza, L. A. Digiampietri, A. C. R. Da Silva, and J. C. Setubal, "Comparative Analyses of Xanthomonas and Xylella Complete Genomes", OMICS: A Journal of Integrative Biology, vol. 9, issue 1, pp. 43 - 76, 03/2005.
2004
Monteiro-Vitorello, C. B., L. E. A. Camargo, M. A. Van Sluys, J. P. Kitajima, D. Truffi, A. M. do Amaral, R. Harakava, J. C. F. de Oliveira, D. Wood, M. C. de Oliveira, et al., "The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli", Molecular Plant-Microbe Interactions, vol. 17, issue 8, pp. 827 - 836, 08/2004.
Moreira, L. M., R. F. De Souza, N. F. Almeida Jr, J. C. Setubal, J. C. F. Oliveira, L. R. Furlan, J. A. Ferro, and A. C. R. Da Silva, "COMPARATIVE GENOMICS ANALYSES OF CITRUS-ASSOCIATED BACTERIA", Annual Review of Phytopathology, vol. 42, issue 1, pp. 163 - 184, 09/2004.
Nascimento, A. L. T. O., A. I. Ko, E. A. L. Martins, C. B. Monteiro-Vitorello, P. L. Ho, D. A. Haake, S. Verjovski-Almeida, R. A. Hartskeerl, M. V. Marques, M. C. Oliveira, et al., "Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis", Journal of Bacteriology, vol. 186, issue 7, pp. 2164 - 2172, 04/2004.
DeMarco, R., A. T. Kowaltowski, A. A. Machado, M. B. Soares, C. Gargioni, T. Kawano, V. Rodrigues, A. M. B. N. Madeira, R. A. Wilson, C. F. M. Menck, et al., "Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni", Journal of Virology, vol. 78, issue 6, pp. 2967 - 2978, 03/2004.
Nascimento, A. L. T. O., S. Verjovski-Almeida, M. A. Van Sluys, C. B. Monteiro-Vitorello, L. E. A. Camargo, L. A. Digiampietri, R. A. Harstkeerl, P. L. Ho, M. V. Marques, M. C. Oliveira, et al., "Genome features of Leptospira interrogans serovar Copenhageni", Brazilian Journal of Medical and Biological Research, vol. 37, issue 4, 2004.
2003
Verjovski-Almeida, S., R. DeMarco, E. A. L. Martins, P. E. M. Guimarães, E. P. B. Ojopi, A. C. M. Paquola, J. P. Piazza, M. Y. Nishiyama, J. P. Kitajima, R. E. Adamson, et al., "Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni", Nature Genetics, vol. 35, issue 2, pp. 148 - 157, 10/2003.
Van Sluys, M. A., M. C. de Oliveira, C. B. Monteiro-Vitorello, C. Y. Miyaki, L. R. Furlan, L. E. A. Camargo, A. C. R. da Silva, D. H. Moon, M. A. Takita, E. G. M. Lemos, et al., "Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa", Journal of Bacteriology, vol. 185, issue 3, pp. 1018 - 1026, 02/2003.
2002
Van Sluys, M. A., C. B. Monteiro-Vitorello, L. E. A. Camargo, C. F. M. Menck, A. C. R. da Silva, J. A. Ferro, M. C. Oliveira, J. C. Setubal, J. P. Kitajima, and A. J. Simpson, "COMPARATIVE GENOMIC ANALYSIS OF PLANT-ASSOCIATED BACTERIA", Annual Review of Phytopathology, vol. 40, issue 1, pp. 169 - 189, 09/2002.
da Silva, A. C. R., J. A. Ferro, F. C. Reinach, C. S. Farah, L. R. Furlan, R. B. Quaggio, C. B. Monteiro-Vitorello, V. M. A. Sluys, N. F. Almeida, L. M. C. Alves, et al., "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities", Nature, vol. 417, issue 6887, pp. 459 - 463, 2002.
2001
Wood, D. W., "The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58", Science, vol. 294, issue 5550, pp. 2317 - 2323, 2001.
2000
Setubal, J. C., A. J. G. Simpson, F. C. Reinach, P. Arruda, F. A. Abreu, M. Acencio, R. Alvarenga, L. M. C. Alves, J. E. Araya, G. S. Baia, et al., "The genome sequence of the plant pathogen Xylella fastidiosa", Nature, vol. 406, issue 6792, pp. 151 - 157, 2000.